Starting phenix.real_space_refine on Thu Feb 13 15:08:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sg1_40450/02_2025/8sg1_40450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg1_40450/02_2025/8sg1_40450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sg1_40450/02_2025/8sg1_40450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg1_40450/02_2025/8sg1_40450.map" model { file = "/net/cci-nas-00/data/ceres_data/8sg1_40450/02_2025/8sg1_40450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg1_40450/02_2025/8sg1_40450.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5669 2.51 5 N 1490 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 3 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8846 At special positions: 0 Unit cell: (94.976, 119.568, 125.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1621 8.00 N 1490 7.00 C 5669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 939.7 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 36.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'R' and resid 36 through 65 removed outlier: 3.929A pdb=" N ILE R 41 " --> pdb=" O ARG R 37 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 92 removed outlier: 3.830A pdb=" N TRP R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 108 through 112 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'R' and resid 127 through 143 removed outlier: 3.802A pdb=" N SER R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 150 removed outlier: 3.641A pdb=" N ASN R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 172 removed outlier: 3.648A pdb=" N ALA R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.921A pdb=" N VAL R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 removed outlier: 5.043A pdb=" N VAL R 231 " --> pdb=" O CYS R 227 " (cutoff:3.500A) Proline residue: R 232 - end of helix Processing helix chain 'R' and resid 256 through 283 removed outlier: 3.617A pdb=" N ILE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 286 No H-bonds generated for 'chain 'R' and resid 284 through 286' Processing helix chain 'R' and resid 291 through 307 removed outlier: 3.758A pdb=" N LEU R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 3.889A pdb=" N ALA R 307 " --> pdb=" O ALA R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 removed outlier: 3.692A pdb=" N MET R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN R 312 " --> pdb=" O ASN R 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 307 through 312' Processing helix chain 'R' and resid 312 through 317 removed outlier: 3.522A pdb=" N VAL R 317 " --> pdb=" O PRO R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 327 removed outlier: 4.031A pdb=" N PHE R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.566A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 21 removed outlier: 4.235A pdb=" N MET G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.853A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.197A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.689A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.576A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 221 through 225 removed outlier: 4.121A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 183 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.403A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.645A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.637A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.286A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.419A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.714A pdb=" N VAL E 156 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 195 through 196 removed outlier: 6.674A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1412 1.31 - 1.44: 2497 1.44 - 1.56: 5028 1.56 - 1.69: 2 1.69 - 1.81: 95 Bond restraints: 9034 Sorted by residual: bond pdb=" C CYS R 272 " pdb=" O CYS R 272 " ideal model delta sigma weight residual 1.236 1.325 -0.089 1.15e-02 7.56e+03 5.93e+01 bond pdb=" C THR R 268 " pdb=" O THR R 268 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.45e+01 bond pdb=" C TRP R 273 " pdb=" O TRP R 273 " ideal model delta sigma weight residual 1.237 1.189 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C PHE R 270 " pdb=" O PHE R 270 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.16e-02 7.43e+03 1.47e+01 bond pdb=" C ILE R 266 " pdb=" O ILE R 266 " ideal model delta sigma weight residual 1.237 1.277 -0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 12136 3.97 - 7.94: 85 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 1 Bond angle restraints: 12231 Sorted by residual: angle pdb=" CA PRO R 275 " pdb=" N PRO R 275 " pdb=" CD PRO R 275 " ideal model delta sigma weight residual 112.00 92.15 19.85 1.40e+00 5.10e-01 2.01e+02 angle pdb=" N MET R 111 " pdb=" CA MET R 111 " pdb=" C MET R 111 " ideal model delta sigma weight residual 112.88 103.50 9.38 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N VAL R 73 " pdb=" CA VAL R 73 " pdb=" C VAL R 73 " ideal model delta sigma weight residual 113.42 105.36 8.06 1.17e+00 7.31e-01 4.75e+01 angle pdb=" N CYS R 112 " pdb=" CA CYS R 112 " pdb=" C CYS R 112 " ideal model delta sigma weight residual 114.56 106.02 8.54 1.27e+00 6.20e-01 4.52e+01 angle pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " pdb=" CG TYR E 236 " ideal model delta sigma weight residual 113.90 103.37 10.53 1.80e+00 3.09e-01 3.42e+01 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4877 17.47 - 34.94: 408 34.94 - 52.41: 91 52.41 - 69.88: 14 69.88 - 87.34: 7 Dihedral angle restraints: 5397 sinusoidal: 2131 harmonic: 3266 Sorted by residual: dihedral pdb=" C TYR E 236 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual -122.60 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual 122.80 144.39 -21.59 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 1375 0.184 - 0.368: 19 0.368 - 0.552: 0 0.552 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA TYR E 236 " pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CB TYR E 236 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA MET R 101 " pdb=" N MET R 101 " pdb=" C MET R 101 " pdb=" CB MET R 101 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA MET R 111 " pdb=" N MET R 111 " pdb=" C MET R 111 " pdb=" CB MET R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1392 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 274 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO R 275 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 271 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C LEU R 271 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU R 271 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS R 272 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 275 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PRO R 275 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO R 275 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR R 276 " 0.025 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1528 2.77 - 3.30: 7933 3.30 - 3.83: 14018 3.83 - 4.37: 17055 4.37 - 4.90: 30530 Nonbonded interactions: 71064 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.246 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR E 151 " pdb=" OE1 GLU E 154 " model vdw 2.263 3.040 nonbonded pdb=" O THR E 145 " pdb=" OG1 THR E 244 " model vdw 2.265 3.040 ... (remaining 71059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 9034 Z= 0.342 Angle : 0.890 19.854 12231 Z= 0.605 Chirality : 0.063 0.921 1395 Planarity : 0.007 0.173 1532 Dihedral : 13.730 87.345 3276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 17.49 % Favored : 80.73 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1105 helix: 0.90 (0.30), residues: 351 sheet: 0.41 (0.31), residues: 281 loop : -0.79 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 273 HIS 0.013 0.001 HIS B 225 PHE 0.029 0.001 PHE L 154 TYR 0.061 0.002 TYR E 236 ARG 0.009 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 275 PRO cc_start: 0.6854 (OUTLIER) cc_final: 0.6601 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7074 (mpt180) REVERT: E 235 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6745 (mm-30) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 1.1152 time to fit residues: 153.6128 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 275 PRO Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 74 ASN R 150 HIS B 175 GLN B 266 HIS B 340 ASN G 59 ASN A 331 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111846 restraints weight = 10371.072| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.38 r_work: 0.3070 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.164 Angle : 0.543 7.389 12231 Z= 0.286 Chirality : 0.042 0.208 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.968 58.917 1324 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 17.17 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1105 helix: 1.51 (0.29), residues: 362 sheet: 0.52 (0.30), residues: 280 loop : -0.79 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE R 259 TYR 0.018 0.001 TYR E 191 ARG 0.003 0.000 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 111 MET cc_start: 0.6891 (tpp) cc_final: 0.6614 (tpp) REVERT: B 215 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 219 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.7101 (mtt-85) REVERT: E 173 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7684 (t) REVERT: E 235 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7013 (mm-30) REVERT: E 236 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.5548 (t80) outliers start: 20 outliers final: 7 residues processed: 115 average time/residue: 1.2056 time to fit residues: 148.4961 Evaluate side-chains 104 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109935 restraints weight = 10532.030| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.39 r_work: 0.3103 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9034 Z= 0.138 Angle : 0.493 7.276 12231 Z= 0.258 Chirality : 0.041 0.195 1395 Planarity : 0.004 0.050 1532 Dihedral : 5.277 54.037 1308 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.83 % Allowed : 17.17 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1105 helix: 1.82 (0.29), residues: 368 sheet: 0.58 (0.31), residues: 267 loop : -0.75 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS E 35 PHE 0.025 0.001 PHE R 169 TYR 0.015 0.001 TYR E 191 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: R 169 PHE cc_start: 0.7395 (t80) cc_final: 0.7188 (t80) REVERT: R 271 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 214 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7427 (mtm180) REVERT: B 215 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 219 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7143 (mtt-85) REVERT: G 28 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7094 (pp) REVERT: A 53 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6531 (mtp) REVERT: E 203 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6725 (mtp180) REVERT: E 235 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7094 (mm-30) REVERT: E 236 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.4972 (t80) REVERT: E 246 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6809 (mp) outliers start: 27 outliers final: 7 residues processed: 132 average time/residue: 1.1150 time to fit residues: 158.5851 Evaluate side-chains 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107660 restraints weight = 10478.330| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.36 r_work: 0.3063 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9034 Z= 0.187 Angle : 0.524 8.435 12231 Z= 0.272 Chirality : 0.042 0.202 1395 Planarity : 0.004 0.057 1532 Dihedral : 5.275 54.563 1307 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.04 % Allowed : 17.28 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1105 helix: 1.83 (0.29), residues: 368 sheet: 0.51 (0.30), residues: 281 loop : -0.82 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE R 169 TYR 0.018 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: R 111 MET cc_start: 0.6783 (tpp) cc_final: 0.6482 (tpp) REVERT: R 271 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.7016 (mp) REVERT: B 214 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7425 (mtm180) REVERT: B 215 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7635 (mm-30) REVERT: B 219 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7084 (mtt-85) REVERT: G 28 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7050 (pp) REVERT: A 53 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6356 (mtp) REVERT: E 203 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6873 (mtp180) REVERT: E 232 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: E 235 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7071 (mm-30) outliers start: 29 outliers final: 10 residues processed: 125 average time/residue: 1.1680 time to fit residues: 156.4629 Evaluate side-chains 113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111143 restraints weight = 10455.537| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.37 r_work: 0.3040 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9034 Z= 0.170 Angle : 0.510 8.140 12231 Z= 0.265 Chirality : 0.042 0.196 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.206 54.152 1307 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.14 % Allowed : 17.80 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1105 helix: 1.86 (0.29), residues: 368 sheet: 0.55 (0.30), residues: 281 loop : -0.83 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 77 HIS 0.005 0.001 HIS E 233 PHE 0.015 0.001 PHE R 190 TYR 0.019 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: R 218 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6651 (ttt) REVERT: R 282 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7175 (tt) REVERT: B 214 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7429 (mtm180) REVERT: B 215 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 219 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.7127 (mtt-85) REVERT: G 28 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7094 (pp) REVERT: A 53 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6409 (mtp) REVERT: E 62 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7296 (p0) REVERT: E 203 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7072 (mtp180) REVERT: E 235 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7118 (mm-30) REVERT: E 246 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6970 (mp) outliers start: 30 outliers final: 13 residues processed: 123 average time/residue: 1.1933 time to fit residues: 157.6702 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109422 restraints weight = 10383.709| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.33 r_work: 0.3074 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9034 Z= 0.146 Angle : 0.511 9.773 12231 Z= 0.260 Chirality : 0.041 0.172 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.090 54.316 1307 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.51 % Allowed : 19.06 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1105 helix: 1.89 (0.29), residues: 368 sheet: 0.54 (0.30), residues: 281 loop : -0.80 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 233 PHE 0.026 0.001 PHE R 169 TYR 0.016 0.001 TYR E 236 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.5993 (m-40) cc_final: 0.5504 (m-40) REVERT: R 218 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6601 (ttt) REVERT: B 214 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7425 (mtm180) REVERT: B 215 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 219 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7106 (mtt-85) REVERT: G 28 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7061 (pp) REVERT: A 53 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6400 (mtp) REVERT: E 203 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7028 (mtp180) REVERT: E 231 MET cc_start: 0.8490 (tpt) cc_final: 0.6953 (tpt) REVERT: E 235 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7082 (mm-30) outliers start: 24 outliers final: 11 residues processed: 120 average time/residue: 1.1962 time to fit residues: 154.2406 Evaluate side-chains 115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107285 restraints weight = 10462.684| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.37 r_work: 0.3045 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9034 Z= 0.190 Angle : 0.530 9.491 12231 Z= 0.270 Chirality : 0.042 0.188 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.141 55.918 1306 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.25 % Allowed : 18.85 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1105 helix: 1.90 (0.29), residues: 368 sheet: 0.53 (0.30), residues: 281 loop : -0.80 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 77 HIS 0.004 0.001 HIS E 233 PHE 0.030 0.001 PHE R 169 TYR 0.018 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.5937 (m-40) cc_final: 0.5497 (m-40) REVERT: R 218 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6629 (ttt) REVERT: B 214 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7453 (mtm180) REVERT: B 215 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 219 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.7083 (mtt-85) REVERT: G 28 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7049 (pp) REVERT: E 62 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7234 (p0) REVERT: E 203 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7036 (mtp180) REVERT: E 235 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7037 (mm-30) REVERT: E 246 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6898 (mp) outliers start: 31 outliers final: 14 residues processed: 124 average time/residue: 1.1531 time to fit residues: 153.5246 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106341 restraints weight = 10601.105| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.35 r_work: 0.3014 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9034 Z= 0.241 Angle : 0.564 11.347 12231 Z= 0.288 Chirality : 0.044 0.210 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.286 57.295 1306 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.83 % Allowed : 18.95 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1105 helix: 1.87 (0.29), residues: 368 sheet: 0.49 (0.30), residues: 280 loop : -0.83 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 77 HIS 0.007 0.001 HIS E 233 PHE 0.014 0.001 PHE E 68 TYR 0.022 0.001 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.5996 (m-40) cc_final: 0.5502 (m-40) REVERT: B 214 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7391 (mtm180) REVERT: B 215 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7635 (mm-30) REVERT: B 219 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7066 (mtt-85) REVERT: G 28 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6979 (pp) REVERT: A 247 MET cc_start: 0.7732 (mtp) cc_final: 0.7473 (mtp) REVERT: E 11 LEU cc_start: 0.8103 (tt) cc_final: 0.7478 (mp) REVERT: E 62 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7237 (p0) REVERT: E 203 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7009 (mtp180) REVERT: E 216 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7493 (p) REVERT: E 231 MET cc_start: 0.8671 (tpt) cc_final: 0.7004 (tpt) REVERT: E 235 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7335 (mt-10) REVERT: E 246 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6969 (mp) outliers start: 27 outliers final: 15 residues processed: 119 average time/residue: 1.2278 time to fit residues: 156.3364 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 88 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106000 restraints weight = 10567.703| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.33 r_work: 0.3033 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9034 Z= 0.238 Angle : 0.569 12.159 12231 Z= 0.290 Chirality : 0.044 0.215 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.342 58.171 1306 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 18.85 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1105 helix: 1.87 (0.29), residues: 368 sheet: 0.43 (0.29), residues: 282 loop : -0.83 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.005 0.001 HIS E 233 PHE 0.028 0.001 PHE R 169 TYR 0.022 0.001 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.931 Fit side-chains REVERT: B 214 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7417 (mtm180) REVERT: B 215 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7676 (mm-30) REVERT: G 28 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7008 (pp) REVERT: A 247 MET cc_start: 0.7810 (mtp) cc_final: 0.7542 (mtp) REVERT: E 62 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7182 (p0) REVERT: E 203 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7136 (mtp180) REVERT: E 231 MET cc_start: 0.8683 (tpt) cc_final: 0.7040 (tpt) REVERT: E 235 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7347 (mt-10) REVERT: E 246 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7027 (mp) outliers start: 26 outliers final: 16 residues processed: 118 average time/residue: 1.2150 time to fit residues: 153.3526 Evaluate side-chains 118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106134 restraints weight = 10486.313| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.32 r_work: 0.3038 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9034 Z= 0.219 Angle : 0.564 14.181 12231 Z= 0.286 Chirality : 0.043 0.209 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.289 58.990 1305 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.09 % Allowed : 19.79 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1105 helix: 1.88 (0.29), residues: 368 sheet: 0.43 (0.30), residues: 282 loop : -0.81 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.004 0.001 HIS E 35 PHE 0.030 0.001 PHE R 169 TYR 0.021 0.001 TYR E 236 ARG 0.004 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.087 Fit side-chains REVERT: B 214 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7479 (mmp80) REVERT: B 215 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 217 MET cc_start: 0.8425 (pmt) cc_final: 0.7835 (ppp) REVERT: G 28 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 247 MET cc_start: 0.7777 (mtp) cc_final: 0.7507 (mtp) REVERT: E 62 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7268 (p0) REVERT: E 203 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: E 235 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7337 (mt-10) outliers start: 20 outliers final: 15 residues processed: 117 average time/residue: 1.2376 time to fit residues: 156.6312 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107870 restraints weight = 10569.352| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.34 r_work: 0.3067 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.156 Angle : 0.531 13.933 12231 Z= 0.269 Chirality : 0.042 0.180 1395 Planarity : 0.004 0.050 1532 Dihedral : 5.115 59.762 1305 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.99 % Allowed : 20.00 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1105 helix: 1.95 (0.29), residues: 366 sheet: 0.49 (0.30), residues: 282 loop : -0.77 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE R 190 TYR 0.017 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6381.51 seconds wall clock time: 113 minutes 28.13 seconds (6808.13 seconds total)